Link OTUs in the HNA population to Productivity

Investigate composition of HNA/LNA populations and relate them to the productivity of Muskegon Lake

Abundance Filtering: 11 OTUs

On Wednesday, April 5th @prubbens ran an analysis without the three outliers. His analysis is in analysis_prod2_remov_outliers.ipynb and pulled out the following 11 OTUs that are associated with heterotrophic productivity:

OTU Phylum Class Order Family Genus Species
Otu000016 Proteobacteria Betaproteobacteria Burkholderiales betII Pnec PnecB
Otu000025 Bacteroidetes Cytophagia Cytophagales bacIII bacIII-A Unclassified
Otu000034 Verrucomicrobia Opitutae Opitutae_vadinHA64 Opitutae_vadinHA64_unclassified Unclassified Unclassified
Otu000040 Verrucomicrobia Verrucomicrobia_unclassified Verrucomicrobia_unclassified Verrucomicrobia_unclassified Verrucomicrobia_unclassified Unclassified
Otu000041 Verrucomicrobia [Spartobacteria] [Chthoniobacterales] verI-B Xip-B1 Unclassified
Otu000042 Planctomycetes Phycisphaerae Phycisphaerales Phycisphaeraceae CL500-3 Unclassified
Otu000050 Planctomycetes Phycisphaerae Phycisphaerales Phycisphaeraceae CL500-3 Unclassified
Otu000067 Bacteroidetes Flavobacteriia Flavobacteriales bacII bacII-A Unclassified
Otu000082 Chlorobi Chlorobia Chlorobiales OPB56 Unclassified Unclassified
Otu000176 Proteobacteria Deltaproteobacteria Bdellovibrionales Bacteriovoracaceae Peredibacter Unclassified
Otu000219 Proteobacteria Betaproteobacteria Burkholderiales betIII betIII-A betIII-A1

CorrFilt: 3 OTUs

On Wednesday, April 5th @prubbens ran an analysis without the three outliers and with an additional correlational filtering step. His analysis is in analysis_prod2_corrfiltering.ipynb and pulled out the following 3 OTUs that are associated with heterotrophic productivity:

OTU Phylum Class Order Family Genus Species
Otu000060 Proteobacteria Alphaproteobacteria Sphingomonadales alfIV alfIV_unclassified Unclassified
Otu000357 Proteobacteria Betaproteobacteria Burkholderiales betI betI-B Rhodo
Otu000124 Verrucomicrobia Opitutae Opitutales Opitutaceae Opitutus Unclassified

Figure 1

Figure 2

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Randomized Lasso

On March 17th, @prubbens performed a randomized lasso in analysis_prod2.ipynb that pulled out the following 12 OTUs that are associated with heterotrophic productivity:

The taxonomy associated with the above OTUs (from data/Chloroplasts_removed/nochloro_taxonomy.tsv) is:

OTU Phylum Class Order Family Genus Species
Otu000123 Proteobacteria Betaproteobacteria Burkholderiales betVII betVII-B betVII-B1
Otu000027 Proteobacteria Betaproteobacteria Burkholderiales betI betI-B Rhodo
Otu000043 Proteobacteria Betaproteobacteria Burkholderiales betI betI-A Lhab-A2
Otu000057 Proteobacteria Betaproteobacteria Methylophilales betIV betIV-A Unclassified
Otu000176 Proteobacteria Deltaproteobacteria Bdellovibrionales Bacteriovoracaceae Peredibacter Unclassified
Otu000005 Cyanobacteria Cyanobacteria SubsectionI FamilyI Unclassified Unclassified
Otu000048 Proteobacteria Alphaproteobacteria Rhodospirillales alfVIII alfVIII_unclassified Unclassified
Otu000040 Verrucomicrobia Verrucomicrobia_unclassified Verrucomicrobia_unclassified Verrucomicrobia_unclassified Verrucomicrobia_unclassified Unclassified
Otu000058 Proteobacteria Gammaproteobacteria Methylococcales gamI gamI_unclassified Unclassified
Otu000067 Bacteroidetes Flavobacteriia Flavobacteriales bacII bacII-A Unclassified
Otu000029 Bacteroidetes Cytophagia Cytophagales bacIII bacIII-B Algor
Otu000025 Bacteroidetes Cytophagia Cytophagales bacIII bacIII-A Unclassified

Figure 3